The Xmalesia project is designed to be collaborative. You can add data directly, or send determinations. The software that runs the database is open source and can be used to host other datasets.
To participate fully, you may need to install some software. Working on this project will be far easier on a linux machine, and the following directions are for a recent Fedora distro. Other distros should be equally easy to prepare (using apt-get, etc).
As root:
# yum install tcsh subversion emacs emacs-nxml-mode xqilla
xmlindent ImageMagick
For validating the main data file, install jing. Place the jing.jar in the following directory (create it if needed): ~/lib/java/. You will also find trang useful for checking the validity of any edits to the RNC schema. E.g.:
java -jar ~/lib/java/trang.jar xmalesia.rnc xmalesia.rng
will raise errors if your RNC file is incorrect.
The full site, including data, is under revision control with Subversion. If you are not using a Linux distro (or Mac OS X), where svn is pre-installed, you will need a SVN client, such as TortoiseSVN. Please read up on the basics of SVN (e.g., the SVN book). Then ask me for a password for checking out and committing versions. The command to get the first checkout is:
mkdir MY_XMAL_COPY cd MY_XMAL_COPY svn checkout --username YOURUSERNAME --password YOURPASSWORD http://svn.phylodiversity.net/xmal/ .
where MY_XMAL_COPY is the name of the directory you want to use for the project. Subsequently, before editing any files, perform a:
svn update
in the root of your working copy (MY_XMAL_COPY). The username and password should have been remembered for this repository.
There are many XML editors, but I suggest using Emacs with nXML mode, because of the on-the-fly validation of the schema. Emacs should automatically enter nXML mode with a .html or .xml suffix. It uses the schemas.xml file to locate the appropriate schema (after looking for foo.rnc in the same directory as foo.xml). Study the xmalesia RNC schema, and/or other parts of the xmalesia.xml datafile before editing. Then just add new components of the data, as needed.
Please maintain the indenting system, using spaces for the indents. Some editors may re-write the whole file, which will cause the entire file to be changed in the versioning system. Apart from requiring large uploads and downloads, this breaks the ability of svn diff to watch for what has changed in the data file.
Please, please validate the main XML data file before you commit any changes. A faulty file will temporarily kill the database. To validate (from the root of your copy of the file tree):
cd bin ./valid
If there are any errors, fix them before committing.
When you are ready to commit your changes, go again to that root directory and:
svn commit -m "Type a useful comment here please"
Using svn hooks, every time you commit to the SVN server, the website is also updated.
Please crop you images to the object of interest. Check the focus. Trash any that are not perfect. Rename the images xx_00000.jpg, where xx is your initials, and 00000 is your unique code for the image.
The http://phylodiversity.net/xmalimg/ image directory contains image files named by appending to a `base name’ (e.g., cw_12345, the creator’s initials followed by the image code) either:
It is very important to maintain this convention, or else the image viewing will not work. To create these files, use ImageMagick. In the directory where your full-size, post-cropping, images live:
tcsh
foreach i (*.jpg)
convert $i -resize 400x400 -font helvetica -pointsize 20 -fill blue
-gravity SouthEast -draw "text 20,20 'Your Name'" {$i:r}.400px.jpg
convert $i -resize 100x100 {$i:r}.100px.jpg
end
Then move the new files to your local copy of the xmalimg directory (see below).
I toyed with keeping the image files under the same version control system, but this approach was just too cumbersome. Instead the image files are all in single directory, accessible via SFTP (secure ftp). Please contact me for the password. There are a few sophisticated programs for syncing over FTP (e.g., FullSync), but an effective syncing can be done with the (usually) pre-installed lftp command-line app. First do a `getting’ of new files, then a `putting’ of your new files. This method assumes that no one else will edit or change the named binary image files once they have been uploaded, so please don’t, unless you created the file, and need to change it.
The command is:
lftp -u xmalimg,PASSWORD -e "cd /home/xmalimg/IMAGES_HERE;
lcd /PATH/TO/LOCAL/XMALIMG/DIR;
mirror --only-missing; mirror -R --only-missing; exit"
sftp://phylodiversity.net
where PASSWORD and (the full) /PATH/TO/LOCAL/XMALIMG/DIR should be changed as appropriate. If you use a simple GUI FTP client (e.g. Cyberduck), set it to only upload and download missing files (`no clobber’), or else you will be waiting for ages. wget and wput can also be used, with the --no-clobber and --skip-existing options, respectively.
Please feel free to use the web-form at the bottom of each individual-page
These instructions are for a Fedora linux distro with GNOME. On a Mac the same may be possible, using fink to install xqilla, although mixing executables with static pages may be tricky without .htaccess control.
<Directory />
Options FollowSymLinks ExecCGI
AllowOverride All
</Directory>
Options Indexes FollowSymLinks ExecCGI
AllowOverride All
UserDir public_html
$ svn checkout http://svn.phylodiversity.net/xmal/ ~/public_html/xmal/.
# chmod a+rx /home # chmod a+rx /home/user # chmod a+rx /home/user/public_html # chmod a+rx /home/user/public_html/xmal # chmod a+rx /home/user/public_html/xmalimg
$ chmod -R go-w ~/public_html
$ cd ~/public_html/xmal/bin $ ./valid
(Last edit: $Id: collab.html 43 2009-03-24 23:53:17Z cwebb $)